[Patchwork-commits] r205 - .git .git/logs .git/logs/refs/heads .git/logs/refs/remotes/origin .git/refs/heads .git/refs/remotes/origin pkg/TAPS/R
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Mar 26 11:37:57 CET 2014
Author: sebastian_d
Date: 2014-03-26 11:37:57 +0100 (Wed, 26 Mar 2014)
New Revision: 205
Modified:
.git/index
.git/logs/HEAD
.git/logs/refs/heads/master
.git/logs/refs/remotes/origin/master
.git/refs/heads/master
.git/refs/remotes/origin/master
pkg/TAPS/R/TAPS.r
Log:
bugfixing bjorn
Modified: .git/index
===================================================================
(Binary files differ)
Modified: .git/logs/HEAD
===================================================================
--- .git/logs/HEAD 2014-03-20 09:35:35 UTC (rev 204)
+++ .git/logs/HEAD 2014-03-26 10:37:57 UTC (rev 205)
@@ -86,3 +86,4 @@
d6dbac6a1a12bfaf8dccbe161c2f509dcc53b73d 0fc6463401c39565b48199c6f4adfe077510620e Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1393856755 +0100 commit: last commit before destroying everything as i try to update kickstart
0fc6463401c39565b48199c6f4adfe077510620e 53a860b490c7ac5501d8bb4f6b95e700491e12d4 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1395307680 +0100 commit: Big upgrades to homepage and genelist
53a860b490c7ac5501d8bb4f6b95e700491e12d4 3e3f8aafc4dd6607de55b08e676598fcdd1ac8c4 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1395307764 +0100 pull: Merge made by the 'recursive' strategy.
+3e3f8aafc4dd6607de55b08e676598fcdd1ac8c4 79c9a62cd0b934e0f252e2fb660c26ffeeeea825 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1395830196 +0100 pull: Fast-forward
Modified: .git/logs/refs/heads/master
===================================================================
--- .git/logs/refs/heads/master 2014-03-20 09:35:35 UTC (rev 204)
+++ .git/logs/refs/heads/master 2014-03-26 10:37:57 UTC (rev 205)
@@ -86,3 +86,4 @@
d6dbac6a1a12bfaf8dccbe161c2f509dcc53b73d 0fc6463401c39565b48199c6f4adfe077510620e Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1393856755 +0100 commit: last commit before destroying everything as i try to update kickstart
0fc6463401c39565b48199c6f4adfe077510620e 53a860b490c7ac5501d8bb4f6b95e700491e12d4 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1395307680 +0100 commit: Big upgrades to homepage and genelist
53a860b490c7ac5501d8bb4f6b95e700491e12d4 3e3f8aafc4dd6607de55b08e676598fcdd1ac8c4 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1395307764 +0100 pull: Merge made by the 'recursive' strategy.
+3e3f8aafc4dd6607de55b08e676598fcdd1ac8c4 79c9a62cd0b934e0f252e2fb660c26ffeeeea825 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1395830196 +0100 pull: Fast-forward
Modified: .git/logs/refs/remotes/origin/master
===================================================================
--- .git/logs/refs/remotes/origin/master 2014-03-20 09:35:35 UTC (rev 204)
+++ .git/logs/refs/remotes/origin/master 2014-03-26 10:37:57 UTC (rev 205)
@@ -83,3 +83,4 @@
d6dbac6a1a12bfaf8dccbe161c2f509dcc53b73d 0fc6463401c39565b48199c6f4adfe077510620e Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1393856763 +0100 update by push
0fc6463401c39565b48199c6f4adfe077510620e bf30fc707ee93417a8fad1f8ab1d8dc7426e128a Sebastian DiLorenzo <S_D at array-47-13.medsci.uu.se> 1395307764 +0100 pull: fast-forward
bf30fc707ee93417a8fad1f8ab1d8dc7426e128a 3e3f8aafc4dd6607de55b08e676598fcdd1ac8c4 Sebastian DiLorenzo <dilorenzo.sebastian at gmail.com> 1395307814 +0100 update by push
+3e3f8aafc4dd6607de55b08e676598fcdd1ac8c4 79c9a62cd0b934e0f252e2fb660c26ffeeeea825 Sebastian DiLorenzo <S_D at array-47-13.medsci.uu.se> 1395830195 +0100 pull: fast-forward
Modified: .git/refs/heads/master
===================================================================
--- .git/refs/heads/master 2014-03-20 09:35:35 UTC (rev 204)
+++ .git/refs/heads/master 2014-03-26 10:37:57 UTC (rev 205)
@@ -1 +1 @@
-3e3f8aafc4dd6607de55b08e676598fcdd1ac8c4
+79c9a62cd0b934e0f252e2fb660c26ffeeeea825
Modified: .git/refs/remotes/origin/master
===================================================================
--- .git/refs/remotes/origin/master 2014-03-20 09:35:35 UTC (rev 204)
+++ .git/refs/remotes/origin/master 2014-03-26 10:37:57 UTC (rev 205)
@@ -1 +1 @@
-3e3f8aafc4dd6607de55b08e676598fcdd1ac8c4
+79c9a62cd0b934e0f252e2fb660c26ffeeeea825
Modified: pkg/TAPS/R/TAPS.r
===================================================================
--- pkg/TAPS/R/TAPS.r 2014-03-20 09:35:35 UTC (rev 204)
+++ pkg/TAPS/R/TAPS.r 2014-03-26 10:37:57 UTC (rev 205)
@@ -172,7 +172,7 @@
Log2$Value <- Log2$Value-median(Log2$Value,na.rm=T) ## Median-centering
allRegions=NULL; #if ('allRegions.Rdata' %in% dir()) load('allRegions.Rdata')
- if (is.null(allRegions)) allRegions <- makeRegions(Log2, alf, segments,matched=matched,allelePeaks=allelePeaks) ## Calculates necessary data for segments (all functions are in this file)
+ if (is.null(allRegions)) allRegions <- makeRegions(Log2, alf, segments,matched=matched,min=30,allelePeaks=allelePeaks) ## Calculates necessary data for segments (all functions are in this file)
save(allRegions,file='allRegions.Rdata')
regs=NULL;# if ('shortRegions.Rdata' %in% dir()) load('shortRegions.Rdata')
if (is.null(regs)) {
@@ -365,13 +365,11 @@
#Test if hg18 or hg19 should be used. length of (hg18 chr19) > (hg19 chr19)
hgtest=regions[regions$Chromosome=="chr19",]
if(hgtest$End[length(hgtest$Chromosome)] > 60000000)
- {
+ {
hg18=T
- }
- else
- {
+ } else {
hg18=F
- }
+ }
#save parameters as strings
parameters=paste("Parameters given: cn2:",sampleInfo$cn2," delta:",sampleInfo$delta," loh:",sampleInfo$loh)
@@ -455,7 +453,7 @@
regs=regs[!is.na(regs$logs),] ### MODDAT MARKUS MAJ 2013
return (regs)
}
-allelicImbalance <- function (data,min,matched=F,allelePeaks=F) {
+allelicImbalance <- function (data,min=30,matched=F,allelePeaks=F) {
if(matched == T ) {
return(2*median(abs(data$Value-.5),na.rm=T))
}
@@ -606,7 +604,7 @@
return (segments)
}
###
-makeRegions <- function(Log2, alf, segments,dataType='Nexus',matched=FALSE,allelePeaks=F) {
+makeRegions <- function(Log2, alf, segments,dataType='Nexus',min=30,matched=FALSE,allelePeaks=F) {
## makeRegions is similar to "regsfromsegs" except regions are not subdivided before calculation of mean Log-R and Allelic Imbalance Ratio.
regions=segments
regions$Chromosome=as.character(segments$Chromosome) ## Chromosome
@@ -2605,11 +2603,10 @@
karyotype_chromsCN <- function(chr,start,end,int,ai,Cn,mCn,hg18,mchr,mpos,mval,schr,spos,sval,t,name='',xlim=c(-1.02,1.82),ylim=0:1, maxCn=8,parameters)
{
- if(hg18==T)
- {
+ if(hg18==T) {
chroms=chroms_hg18
chromData=chromData_hg18
- }
+ }
#Get ideogram
#ideogram=getIdeogram()
@@ -2706,8 +2703,7 @@
par(oma = c(0,0,0,0))
par(mgp =c(0.5,0.25,0))
- if(c!=23)
- {
+ if(c!=23) {
#Whole genome overview plot
#Note that we are plotting chrY in the background, despite the fact that it is not an "active" chromosome.
plot(c(int[notix],int[ix]),c(ai[notix],ai[ix]),
@@ -2720,9 +2716,7 @@
col = c(col[notix],col[ix]),
xlim = c(-1,1.5),
ylim = ylim)
- }
- else
- {
+ } else {
plot(int[notix],ai[notix],
pch=16,
cex=size[notix],
@@ -2736,12 +2730,9 @@
}
xix=chr=="chrX"
- if(c!=23)
- {
+ if(c!=23) {
points(int[xix],ai[xix],pch=4,col='#46464680')
- }
- else
- {
+ } else {
points(int[xix],ai[xix],pch=4,col=col[ix])
}
@@ -3779,6 +3770,7 @@
# sampleData <- read.csv('SampleData.csv',sep='\t',header=T,colClasses=c('character',rep('numeric',4)),stringsAsFactors=F)
sampleData <- read.csv('SampleData.csv',sep='\t',header=T,stringsAsFactors=F)
+ if(any(colnames(sampleData) %in% c('MAPD','MHOF'))) sampleData <- sampleData[,1:5]
sampleDataOri <- sampleData
if(any(T == sampleData$done)) {
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